Update AppendCiteSeq for newer versions

bbimber · bbimber · commit 6545d9526778 · 2024-08-07T06:10:20.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java
@@ -132,7 +132,14 @@ protected Map<Integer, File> prepareCountData(SingleCellOutput output, SequenceO
 
                 if (dropAggregateBarcodes)
                 {
+                    // NOTE: this is the location in CellRanger <= 6.x
                     File aggregateCountFile = new File(existingCountMatrixUmiDir.getParentFile(), "antibody_analysis/aggregate_barcodes.csv");
+                    if (!aggregateCountFile.exists())
+                    {
+                        // This is the location for >= 7.x
+                        aggregateCountFile = new File(existingCountMatrixUmiDir.getParentFile(), "aggregate_barcodes.csv");
+                    }
+
                     if (!aggregateCountFile.exists())
                     {
                         throw new PipelineJobException("Unable to find aggregate count file: " + aggregateCountFile.getPath());

Original file line number	Diff line number	Diff line change
`@@ -132,7 +132,14 @@ protected Map<Integer, File> prepareCountData(SingleCellOutput output, SequenceO`
`132`	`132`
`133`	`133`	`if (dropAggregateBarcodes)`
`134`	`134`	`{`
	`135`	`+ // NOTE: this is the location in CellRanger <= 6.x`
`135`	`136`	`File aggregateCountFile = new File(existingCountMatrixUmiDir.getParentFile(), "antibody_analysis/aggregate_barcodes.csv");`
	`137`	`+ if (!aggregateCountFile.exists())`
	`138`	`+ {`
	`139`	`+ // This is the location for >= 7.x`
	`140`	`+ aggregateCountFile = new File(existingCountMatrixUmiDir.getParentFile(), "aggregate_barcodes.csv");`
	`141`	`+ }`
	`142`	`+`
`136`	`143`	`if (!aggregateCountFile.exists())`
`137`	`144`	`{`
`138`	`145`	`throw new PipelineJobException("Unable to find aggregate count file: " + aggregateCountFile.getPath());`